9K93 | pdb_00009k93

Cryo-EM structure of human signal peptide peptidase like 2A (SPPL2a) in complex with L685,458

• PDB DOI: https://doi.org/10.2210/pdb9K93/pdb
• EM Map EMD-62186: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Insect expression vector pBlueBachsGCA1
• Mutation(s): No 


• Deposited: 2024-10-25 Released: 2025-10-29 
• Deposition Author(s): Zhou, R., Huang, G., Guo, X., Wang, J., Ge, X., Shi, Y.
• Funding Organization(s): National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into human signal peptide peptidase

Zhou, R., Huang, G., Guo, X., Wang, J., Ge, X., Shi, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 58.86 kDa 
• Atom Count: 2,307 
• Modeled Residue Count: 282 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal peptide peptidase-like 2A	A	520	Homo sapiens	Mutation(s): 0  Gene Names: SPPL2A, IMP3, PSL2, PSEC0147 EC: 3.4.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TCT8 (Homo sapiens) Explore Q8TCT8  Go to UniProtKB:  Q8TCT8
PHAROS:  Q8TCT8 GTEx:  ENSG00000138600

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FTO (Subject of Investigation/LOI)	B [auth A]	~{tert}-butyl ~{N}-[(2~{S},3~{R},5~{R})-6-[[(2~{S})-1-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-oxidanyl-6-oxidanylidene-1-phenyl-5-(phenylmethyl)hexan-2-yl]carbamate C39 H52 N4 O6 MURCDOXDAHPNRQ-ZJKZPDEISA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Zhou, R., Huang, G., Guo, X., Wang, J., Ge, X., Shi, Y.

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Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2020YFA0509300

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release